Arouna Kone's quickfire double at the end of the first half gave them an advantage they quickly made decisive after the break when Maynor Figueroa combined with Franco Di Santo for the defender to net a rare goal.
Reading's afternoon quickly deteriorated and when Pavel Pogrebnyak saw red after 55 minutes the visitors were already banking a win to inspire belief they are again on course to beat the drop.
But McDermott felt Kone's opener should not have stood due to a handball from Gary Caldwell in the build-up.
McDermott claimed the Scotland defender had admitted to him he had touched the ball before it broke for Figueroa, whose goal-bound shot went in off Kone's back.
"It definitely should not have been given," he said. "I just spoke to Caldwell and he said himself he's handballed it. He knows he's handballed it. Unfortunately the ref hasn't seen it. It was a bad day. They've had a good day and we've had a bad day."
Reading did have their chances to go ahead after controlling possession before Kone's double strike. Hope Akpan headed over unmarked while Jimmy Kebe lashed an angled shot into the side-netting before Wigan got going.
"The first 43 minutes there wasn't too much in the game," McDermott said. "If Jimmy scores then maybe it's a different game. The goal changes the game. They got a real spring in their step once they scored. But we didn't do the right things at the right time. We didn't get the details right.
"There are plenty of things you can look at. I'm going to move on quickly from that game. It's the only thing you can do in a situation like that.
"We've got 11 games to go now. We'll have a lot of good days in those 11 hopefully."